I never really liked Mikuru because it's always the same thing with her (I.e: scared little girl routine, OMG! shes so cute crap.) But changing her into a boy who's had to endure constant suffering throughout school makes her a more relatable character and more interesting character to me. I actually wish the author would have made Mikuru's character more like this.

Good story. You had an interesting take on Mitsuru's life; it sucks to be treated like a pretty-face dress-up doll, but it sucks even worse when the victim is rubbing up against ingrained prejudice about proper behavior. I notice that Kyon wasn't as interested in protecting a cute boy as he was in protecting a cute girl. Kyon doesn't take on the importance in Mitsuru's life that he has in Mikuru's existence. That fact doesn't surprise me, though. Canonically Kyon is a dick at times. (I can give you a few examples of if you want, but they're not hard to find.) All in all, this is a good concept and it's written well.

Ah the Genderbending of Haruhi Suzumiya... I agree that Mitsuru has always been a huge source of debate and your portrayal of him fits quite nicely in my opinion. I also see it as a 'what if Mikuru wasn't so popular?' type of story since Mitsuru isn't very well liked and bullied all the time like Mikuru probably would be.

All in all, it was a very good one-shot and does showcase the inner thoughts of one of the characters we really don't know about (aka. Mikuru, Itsuki, Tsuruya, etc).